It is widely acknowledged that the phase noise of an optical frequency comb primarily stems from the common mode (carrier-envelope) and the repetition rate phase noise. However, owing to technical noise sources or other intricate intra-cavity factors, residual phase noise components, distinct from the common mode and the repetition rate phase noise, may also exist. We introduce a measurement technique that combines subspace tracking and multi-heterodyne coherent detection for the separation of different phase noise sources. This method allows us to break down the overall phase noise sources associated with a specific comb-line into distinct phase noise components associated with the common mode, the repetition rate and the residual phase noise terms. The measurement method allow us, for the first time, to identify and measure residual phase noise sources of a frequency modulated mode-locked laser.